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University of Texas MD Anderson Cancer Center
Statistical Issues in Proteomic Research
Jeffrey S. Morris Thu, 31 Jul 2008 11:03:24 -0700
Microproteomics: Analysis of protein diversity in small samples
Howard B. Gutstein Fri, 13 Jun 2008 14:38:53 -0700
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Jeffrey S. Morris Tue, 04 Dec 2007 09:44:53 -0800
Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust, and reproducible methods for detecting, matching, and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels, and finally quantifying each spot by calculating normalized spot volumes. This approach is time con-suming, error-prone, and frequently requires extensive manual edit-ing, which can unintentionally introduce bias into the results.Results: We introduce a new method for spot detection and quanti-fication called Pinnacle that is automatic, quick, sensitive and spe-cific, and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller CVs. More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.
Laser capture sampling and analytical issues in proteomics
Howard Gutstein Tue, 04 Dec 2007 09:35:54 -0800
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
Statistical contributions to proteomic research
Jeffrey S. Morris Wed, 04 Apr 2007 12:55:09 -0700
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the key statistical principles that should guide the experimental design and analysis of such studies.
Wavelet-based functional mixed model analysis: Computational considerations
Richard C. Herrick Wed, 04 Apr 2007 12:48:45 -0700
Wavelet-based Functional Mixed Models is a new Bayesian method extending mixed models to irregular functional data (Morris and Carroll, JRSS-B, 2006). These data sets are typically very large and can quickly run into memory and time constraints unless these issues are carefully dealt with in the software. We reduce runtime by 1.) identifying and optimizing hotspots, 2.) using wavelet compression to do less computation with minimal impact on results, and 3.) dividing the code into multiple executables to be run in parallel using a grid computing resource. We discuss rules of thumb for estimating memory requirements and computation times in terms of model and data set parameters. We present examples and benchmarks demonstrating that it is practical to analyze very large data sets with readily available computing resources. This code is freely available on our website.
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Statistical Issues in Proteomic Research
Jeffrey S. Morris Thu, 31 Jul 2008 11:03:24 -0700
Microproteomics: Analysis of protein diversity in small samples
Howard B. Gutstein Fri, 13 Jun 2008 14:38:53 -0700
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Jeffrey S. Morris Tue, 04 Dec 2007 09:44:53 -0800
Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust, and reproducible methods for detecting, matching, and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels, and finally quantifying each spot by calculating normalized spot volumes. This approach is time con-suming, error-prone, and frequently requires extensive manual edit-ing, which can unintentionally introduce bias into the results.Results: We introduce a new method for spot detection and quanti-fication called Pinnacle that is automatic, quick, sensitive and spe-cific, and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller CVs. More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.
Laser capture sampling and analytical issues in proteomics
Howard Gutstein Tue, 04 Dec 2007 09:35:54 -0800
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
Statistical contributions to proteomic research
Jeffrey S. Morris Wed, 04 Apr 2007 12:55:09 -0700
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the key statistical principles that should guide the experimental design and analysis of such studies.
Wavelet-based functional mixed model analysis: Computational considerations
Richard C. Herrick Wed, 04 Apr 2007 12:48:45 -0700
Wavelet-based Functional Mixed Models is a new Bayesian method extending mixed models to irregular functional data (Morris and Carroll, JRSS-B, 2006). These data sets are typically very large and can quickly run into memory and time constraints unless these issues are carefully dealt with in the software. We reduce runtime by 1.) identifying and optimizing hotspots, 2.) using wavelet compression to do less computation with minimal impact on results, and 3.) dividing the code into multiple executables to be run in parallel using a grid computing resource. We discuss rules of thumb for estimating memory requirements and computation times in terms of model and data set parameters. We present examples and benchmarks demonstrating that it is practical to analyze very large data sets with readily available computing resources. This code is freely available on our website.
Sites:
South Cumbria Cancer Network: Provides information on available local services in this multi-site UK region. Includes links to other related resources.Alegent Health: Head and Neck Cancer Center: Focus on treatment, reconstruction, rehabilitation and support. Multi-location facilities in Iowa and Nebraska.
American Institute for Cancer Ablation: Extension of the McCollough Institute in Golf Shores, Alabama that offers radiofrequency therapy.
Arlington Cancer Center: Oncology services include diagnosis, treatment, research, education and support services. Located in the Dallas/Fort Worth, Texas area.
Bay Area Tumor Institute: Bay Area Tumor Institute offers free programs in cancer research, prevention, education, and consultation to San Francisco East Bay citizens.
Blount Memorial Hospital: Cancer Care: Blount Memorial Hospital offers comprehensive cancer services designed to meet the needs of both the patient and family.
Bon Secours St. Mary's Hospital: Cancer Care Center: The Bon Secours Richmond Health System support the healthcare need of central Virginia. Find out more about how we serve the community.
Burzynski Clinic: New innovative comprehensive gene therapy cancer treatment designed to treat the total person not just the cancer. Experience a gentle way to treat cancer today.
California Hematology Oncology Medical Group: Los Angeles center which offers traditional and complementary medicine.
Cancer Center of Iowa: Multi-location practice located in Des Moines, Iowa.
Cancer Center of Santa Barbara: Radiation Oncology, Hematology/Medical Oncology and Nuclear Medicine. Support services including: clinical research trials, wellness programs, counseling and cancer support groups.
Cancer Centers of Florida: At Cancer Centers of Florida, we take pride in providing our patients with treatment centers that are both comfortable and convenient. Serving Lake, Orange, Osceola, Polk and Seminole Counties, we have multiple centers that offer care to patients in their immediate community. As part of U....
Cancer Centers of North Carolina: Cancer Centers of North Carolina has a range of advanced treatments, including radiation, chemotherapy, and access to clinical trials.
Cancer Centre for the Southern Interior: City of Hope is committed to Helping bCancer/b patients worldwide.
Cancer Treatment Centers of America: Learn about a complete range of traditional and new innovative cancer treatment therapies designed to treat your mind, body, and soul, not just your cancer. Start fighting today.
CancerCare: Information about these medical facilities which provide care to the North Lancashire and South Lakeland areas in England.
Cedars-Sinai Oncology Program: Welcome to the Samuel Oschin Comprehensive Cancer Treatment Institute at Cedars-Sinai Medical Center.
Charleston Cancer Center: Charleston Cancer Center in Charleston South Carolina
Evansville Cancer Center: Cancer resource site providing information on radiation and medical oncology, as well as our patient services, physicians, and links to other cancer related sites.
Fox Valley Hematology and Oncology: Multi-site oncology center based in Illinois. Provides information on services, physician profiles and contact details.
Geffen Cancer Center and Research Institute: Domain name renewal and affordable web hosting packages from Network Solutions
Health Alliance Cancer Services: Health Alliance cancer centers, staff and physicians offer a multidisciplinary approach to the prevention, diagnosis and treatment of cancer including everything from clinical trials to cancer information to support groups.
Hendrick Medical Center: Hendrick Medical Center in Abilene, Texas. Providing treatment for Cancer and Cancer.
Jay Monahan Center for Gastrointestinal Health: Screening, diagnosis, treatment and support for gastrointestinal cancers offered at the New York-Presbyterian Weill Cornell Medical Center.
Jewish Hospital: Lung Cancer Center: Jewish Hospital HealthCare Services' regional network of more than 50 health care facilities provides complete health care services in Kentucky and southern Indiana including: hospitals, emergency air ambulance, assisted living, home health care, outpatient care, nursing home care, occupational h...
Kansas City Cancer Centers: Kansas City Cancer Center
Lewis Family Cancer Care Center: Provides comprehensive cancer care and support in a community setting.
London Regional Cancer Centre: Affiliate of the University of Western Ontario providing a full range of care including basic and translational research. Located in London, Ontario.
Louisiana Oncology Associates: Home of Louisiana Oncology Associates, your Acadiana cancer specialists. Creating Wellness at Home
Mary Bird Perkins Cancer Center: A multi-site community owned oncology facility located in Louisiana.
Memphis Cancer Center: 2b interactive's mission is to work closely with you to develop and maintain a successful online venture through a well defined and strategic internet marketing campaign, including strategic planning, web site development and enhancement, technical services, interactivity, and online marketing.
Missouri Cancer Associates: Multi-site comprehensive diagnostic, treatment and support capability. Headquartered in Columbia, Missouri with other locations in the north and mid-state regions.
Netherlands Cancer Institute: Head and Neck Cancer: This site contains information on cancer in the head and neck and treatment in the netherlands Cancer Institute.
Northern Arizona Hematology and Oncology: We provide consulting services and therapy for patients with malignant diseases and hematologic disorders. We are a comprehensive cancer treatment center based in Flagstaff Arizona using the latest technology and pharmaceutical advancements. We strive to make advanced state of the art cancer care...
Northern Cancer Network UK: Information about diagnosis, treatment and support from this regional network of providers and hospitals in the north of England.
Northwest Arkansas Radiation Therapy Institute: Northwest Arkansas Radiation Therapy Institute
Northwestern Ontario Regional Cancer Centre: Thunder Bay Regional Health Sciences Centre
Oncology Associates of Bridgeport: Oncology Associates of Bridgeport, PC
Oncology Center of Central Baltimore: At the Oncology Center of Central Baltimore, Dr. Stanley D. Walker and Dr. Suman B. Rao offer knowledge that gets results, with more than 25 years of clinical and research experience between them.
Pelican Center: The Pelican Cancer Foundation is dedicated to world class precision surgery for treating the many common cancers that occur within the pelvic region. It has the highest cure rates for rectal cancer published anywhere in the world and the lowest percentage of permanent colostomies.
Penrose Cancer Center: Penrose Cancer Center
Puget Sound Cancer Centers: Edmonds and Seattle, physician information, cancer information, insurance information, clinical research, online maps, relevant news and legislation,Ó>
Rocky Mountain Cancer Centers: RMCC is Colorado's largest and most comprehensive provider of cancer care with 20 locations and more than 50 physicians throughout the state.
Saint Mary's Cancer Center: Outlines institutional programs including screening, prevention, diagnosis, treatment and research. Located in Grand Rapids; serving West Michigan.
Sarah Cannon Cancer Center: Affiliated facilities in mid-Tennessee and southern Kentucky. Includes informational guides to chemotherapy and breast cancer.
Seattle Cancer Care Alliance: Learn about internationally renowned cancer treatment programs for, breast cancer, skin cancer, lung cancer, leukemia, prostate cancer, colon cancer, ovarian cancer, lymphoma, melanoma, cervical cancer, Stem Cell transplantation, liver cancer, pediatric cancers, testicular cancer, pancreatic canc...
Seattle Cancer Treatment and Wellness Center: Integrative care model: oncologists working with naturopathic and Chinese medicine practitioners. Contact details provided.
South Carolina Oncology Associates: South Carolina Oncology Associates (SCOA), the most comprehensive private cancer treatment center in South Carolina.
Stoke Mandeville Hospital: The Cancer Care and Haematology Fund based at Stoke Mandeville Hospital provides patients with medical treatment, including chemotherapy, clinic review, treatment for blood disorders, including leukaemia and lymphoma, and complementary therapy. Patients and their families also receive emotional s...
Sutter Cancer Center: Information about Cancer Services at Sutter Health Sacramento Sierra Region.
Texas Cancer Institute: Treatment and research center at St. Luke's Episcopal Hospital in Houston. Provides patient information and a services overview.
The Center for Cancer Care and Research: St. Louis: The Center for Cancer Care and Research on the Web.
The Oncology Center: Orange, California: The Oncology Center is Orange County's leading cancer center with all patient diagnostics, treatments and support services in one location. Comprehensive services include: imaging, surgery, chemotherapy, complementary medicine, social services, and volunteers.
The Saint Francis Care Regional Cancer Center: Saint Francis Hospital and Medical Center recognizes cancer as a major national health problem. The Cancer Clinical Program is a commitment to excellence within a cancer center frame-work, incorporating cancer prevention, detection, evaluation, treatment, rehabilitation, teaching and research.
Thiruvananthapuram Regional Cancer Centre: A facility that serves the State of Kerala and adjoining areas of Tamil Nadu and Karnataka, India. Describes the diagnostic, research and treatment programs.
Thompson Cancer Survival Center: Thompson Cancer Survival Center is an outpatient facility located in Knoxville, TN offering state-of-the-art cancer treatment, including clinical trials with investigational drugs for patients who do not respond to standard treatments.
University of Iowa: Department of Radiation Oncology: Overview of cancer types, treatments, staff, post-graduate training and specialized programs.
US Oncology Cancer Centers: Affiliated facilities located in many regions of the United States. Gives physician profiles, photos, location and contact information.
Virginia Mason Medical Center: Cancer Institute: The file your browser requested could not be found on our servers. We have recently changed our web site and we may have moved around, renamed, or deleted certain files.
Virginia Oncology Associates Cancer Treatment Center: Virginia Oncology Associates is a private practice of physicians specializing in the diagnosis and treatment of cancer.
Western Washington Cancer Treatment Center: Diagnostic and treatment facility located in Olympia, Washington.
This directory is based on the Open Directory and may have been modified